Livestock often undergo significant exposure to transport and handling, co-mingling, auction and some time off feed and water. Collectively, these events can impede the immune system and can result in a significant incidence of disease. Such events can have considerable economic impact, for example, on the agricultural industry both with respect to health treatment costs and animal performance. Recent research has resulted in an increased understanding of the importance of animal management factors, such as transport and ante-mortem handling, in influencing both animal welfare and the food quality arising from such animals. It is known that disease and stress can have a dramatic, negative impact on animal welfare parameters and performance as well as meat quality and yield and hence the economics of the animal industries.
As would be known to a person of skill in the art, a number of diseases, such as Bovine Viral Diarrhea (BVD) type 1 and 2, Infectious Bovine Rhinotracheitis (IBR), Corona Virus, Bovine Para-Influenza (PI3) and Bovine Respiratory Syncytial Virus (BRSV), can impact livestock populations. One such disease complex, known as bovine respiratory disease (BRD), refers to a host of complex diseases, and is generally used to refer to an animal displaying an undifferentiated fever and/or other clinical signs (e.g. respiratory distress, lethargy, and loss of appetite).
The presence of BRD in intensively raised calves has caused a dependence on antibiotic treatments (including mass treatments), which, in turn, has led to a concern for the promotion of antibiotic resistant microbes. Indeed, the ability to treat BRD in cattle is becoming more difficult due to the emergence of resistant microbes (for e.g., pneumonia), or new zoontic diseases in multiple sourced, co-mingled cattle. Furthermore, recent reports have shown substantial contamination of carcass and meat products with antibiotic resistant strains of bacteria such as E. coli. 
The effectiveness of treating livestock diseases, such as BRD, can depend upon the ability to detect, diagnose and treat affected animals early. The ability to achieve early detection will depend upon the information available and on the reliability of that information. For instance, when used alone, traditional clinical signs of disease provide poor diagnostic results because clinical symptoms often occur late into the course of the illness. Further, many diagnostic techniques, such as the use of acute phase proteins or hematology assessment, require the capture and invasive, in vivo collection of biological samples, which result in the significant cost of analysis and time. The requirement of the capture (and therefore restraint) of the animal in order to collect a biological sample causes stress, and the process itself is therefore introducing inaccuracies into the data collected.
Recent research has focused on alternative approaches to non-invasively determine the early identification and onset of disease in cattle. One such approach is infrared thermography, which can be used as a means of detecting the dissipation of heat in animals. Thermography operates on the principle that infrared radiation can be utilized to observe radiated heat loss and to provide an early indicator of fever because up to ˜60% of the heat loss from an animal can occur in infrared ranges. The technology has been demonstrated to be effective in non-invasive identification of transport and other environmental stressors that can alter an animal's heat loss.
Another approach to non-invasive disease analysis is the commonly used “pen-checking” approach, wherein the animal caregiver observes the animal on a daily basis to detect any abnormal behavioural patterns, or clinical signs of illness (e.g. decrease in eating due to loss of appetite; see Table 1 for further examples of behavioural benchmarks). Although non-invasive, pen-checking is highly inaccurate particularly during the early stages of disease onset and leads to false-positive and false-negative results because it depends upon the skill and observations of the caregiver. Further, it is known that animals often do not display overt signs of illness (that would be detectable to a caregiver) until later in the progression of the disease, resulting in an increased risk of infection of healthy animals in a population, particularly where the animals share a source of food and water.
TABLE 1PRIOR ARTCommonly-used clinical scores used in the bovine respiratory disease (BRD)early disease detectionClinical Score Assessment012345Disposition,MovingSlightlyModerateHangingProstrate,DeathLethargyarounddepressedlethargyback fromRecumbentandwell withappearance,andthe rest ofor abnormalBehaviournormalHolds headdepression,the herd,posture,posture,slightlyHolds headRecumbentNotContent,lower thanlow, Droopyorinterested inNonormal, Mildears, Slowabnormalsurroundings,signs ofanorexiato rise,posture,WeaknesslethargyStiffLargelymovements,depressedAnorecticRespiratoryNormalVery fineFine crackleMediumCourseMarkedInsultbreathcrackleand/orcracklecracklesrespiratorysoundsand/ormoderateand/orand/ordistressmoderatenasalmoderatesevereand/or lungcoughdischargeto severedischargeconsolidationandviscouswithmoderatenasalrespiratorycoughdischargedistress andwith coughobtundedlung soundsDigestiveNoMild orModerateModerateSevereSevereInsultinsult,slightdiarrheato severediarrhea, anddiarrhea andNormaldiarrheawith 10%diarrhealess thannot eating,eatingwith slightdehydrationwith 10% or10% ofnot drinkinganddehydrationandless of feednormal feedanddrinkingand reducedreducedintake andintakedehydratedeatingfeed intakemore than10%dehydration
It is also known that the identification of non-disease states in animals is important to the agricultural industry as well as to zoo and wildlife biology settings. There are many biological events in an animal's life that influence a plethora of biometric measurements and characteristics expressed. Some of these events are normal biological functions an animal will display such as when they adapt to a changing environmental temperature, a changing growth period or a changing endocrine event including puberty or estrus. Other events are less common and will include the onset of a disease state. In either disease or non-disease states the animal will be considered to be in a biologically important, non-steady state during these periods. These biologically important states may have, for example, agriculturally important consequences and implications.
Growth efficiency in animals is often defined as the gain in a particular tissue type such as muscle or milk compared to the input of resources such as feed and water. In addition to disease states, growth efficiency is an important attribute in animal agriculture as competition for limited resources increases. However, measuring growth efficiency has always been a challenge. One of the more accurate methods to monitor growth efficiency is to use indirect calorimetry which measures exactly the amount of oxygen and energy used by an animal for a given increase in gain of a specific tissue while noting that the metabolism will also give off heat (Kleiber, M. 1961. The fire of life—an introduction to animal energetics. John Wiley & Sons, Inc). Alternatively, growth efficiency can be monitored by measuring the actual feed consumed by an animal and the growth that resulted or measuring the so called gain to feed ratio (Kleiber, M. 1961. The fire of life—an introduction to animal energetics. John Wiley & Sons, Inc).
A more recent approach to monitoring growth efficiency has been to monitor the so called residual feed intake (RFI) which fundamentally is a comparison of the measured feed to gain against a known estimate for feed to gain based on scientifically accepted formulas (Basarab et al. 2003, 2007 see below). However, this later method, while reasonably accurate, requires a lengthy seventy days or more feed monitoring period which is both expensive and impractical.
It is also known that the identification of reproductive states in animals is important to biology in general and to the agricultural industry specifically. For example, reproductive states such as onset of puberty and estrus are important to identify for the purposes of reproductive efficiency, and therefore agricultural efficiency. It is known in the art that the onset of puberty and estrus are characterised by behavioural estrus which includes an increased restlessness of the animal.
There is therefore a need for non-invasive, early and accurate means of identifying biologically important states in animals. Furthermore, there is a need for a non-invasive detection means that are capable of identifying diseased animals, even in populations where there is a low prevalence of the disease.